Polynucleotide helical

N 117 "A Configurational Interpretation of the Axial Phosphate Spacing in Polynucleotide Helices and Random Coils"... 

Molecular models of polynucleotide helices consistent with the observed axial rise per nucleotide (7z) and its turn angle ( ), which are accurately measurable from the fibre... 

Polynucleotide helices are known to dissociate reversibly (Lipsett et al., 1960 Doty et al., 1959) upon heating, the melting temperature depending upon the polymers used and upon the kind and concentration of salt. By using heated solutions. Miles (1960) has followed the thermal dissociation of these three-stranded helices (Fig. 12.9 and Table 12.3) by their infrared spectra. The hot solution of tetra A -I- 2 poly U... 

Double heliees ean be formed between one DNA and one RNA polynucleotide. Helices of this kind are of great importanee in biology and occur, for example, in transcription and in antisense oligonucleotides (Chapter 11.6). 

It is of interest to note that the model proposed by these authors for poly-L-lysine-DNA complex is quite different from the RNA to poly-L-lysine model described above. They concluded that a molecular model similar to that of deoxyribonucleoprotamine proposed by Wilkins (1956) would be acceptable for the poly-L-lysine DNA complex. In this model, an almost fully extended polypeptide chain also winds helically around the double-stranded polynucleotide chains. Unlike the RNA model, however, the pitch of the polypeptide helix is the same as that of the polynucleotide helices This model requires one amino acid residue per one nucleotide residue, i.e., NH tP = 1 1, as is experimentally observed. On the other hand, this... 

In addition to hydrogen bonding between the two polynucleotide chains the double helical arrangement is stabilized by having its negatively charged phosphate groups on the outside where they are m contact with water and various cations Na" Mg and ammonium ions for example Attractive van der Waals forces between the... 

By analogy to the levels of structure of proteins the primary structure of DNA IS the sequence of bases along the polynucleotide chain and the A DNA B DNA and Z DNA helices are varieties of secondary structures... 

The DNA isolated from different cells and viruses characteristically consists of two polynucleotide strands wound together to form a long, slender, helical molecule, the DNA double helix. The strands run in opposite directions that is, they are antiparallel and are held together in the double helical structure through interchain hydrogen bonds (Eigure 11.19). These H bonds pair the bases of nucleotides in one chain to complementary bases in the other, a phenomenon called base pairing. 

The exact nature of the lesion in DNA is unknown, and so is the type of DNA that is attacked. Recent X-ray crystallographic studies, as well as other physicochemical studies, have made it clear that DNA is not simply a polynucleotide, folded as Watson and Crick (106) proposed. There are three main conformational types of DNA they each keep the hydrogen-bonded bases in the center of the helix, but may tilt them by a "propellor twist," may slide them from the center of the helix in the plane of the base pairs, and may vary the amount of rotation from one base pair to the next up the helical axes. 

The molecule consists of two polynucleotide strands that are wrapped around each other in a helical fashion. 

The question of energy transfer is introduced also by the fact that polynucleotides frequently exist not only in single-strand forms but also entirely or partially as double-strand helices in which pyrimidine residues on one chain are hydrogen bonded to purine residues on the other chain. The reactivity of the pyrimidine residue can be strongly affected by the presence of its purine partner. An example of this will be found further on. 

As Figure 8-16 shows, the two antiparallel polynucleotide chains of double-helical DNA are not identical in either base sequence or composition. Instead they are complementary to each other. Wherever adenine occurs in one chain, thymine is found in the other similarly, wherever guanine occurs in one chain, cytosine is found in the other. 

Complexes between chiral polymers having ionizable groups, and achiral small molecules become, under certain conditions, optically active for the absorption regions of the achiral small molecules. Dyes such as acridine orange and methyl orange have been used as achiral species, since they are in rapport with biopolymers through ionic coupling. This phenomenon has been applied to the detection of the helix chirality in poly-a-amino acids, polynucleotides, or polysaccharides when instrumental limitations prevent direct detection of the helices. 

A few recent NMR investigations of polynucleotides include studies of triple-helical DNA,689 Holliday junctions,290 double-stranded oligonucleotides containing adducts of carcinogens,690 691 of hairpin loops with sheared A A and G G pairs,692 and of proton exchange in both imino and amino groups.693... 

Whereas proteins have their low energy absorption band at 280 nm, polynucleotides typically have maxima at 260 nm (38,500 cm ). A phenomenon of particular importance in the study of nucleic acids is the hypochromic effect. In a denatured polynucleotide the absorption is approximately the sum of that of the individual components. However, when a double helical structure is formed and the bases are stacked together, there is as much as a 34% depression in the absorbance at 260 nm. This provides the basis for optical measurement of DNA melting curves (Fig. 5-45).45,86 The physical basis for the hypochromic effect is found in dipole-dipole interactions between the closely stacked base pairs.7,86,87... 

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